| Abstract
| - Car−Parrinello molecular dynamics simulations of the flexibility of isolated DNA bases have been carriedout. The comparison of lowest ring out-of-plane vibrations calculated by using MP2/cc-pvdz and BLYP/PWmethods reveals that the DFT method with the plane wave basis set reasonably reproduces out-of-planedeformability of the pyrimidine ring in nucleic acid bases and could be used for reliable modeling ofconformational flexibility of nucleobases. The conformational phase space of pyrimidine rings in thymine,cytosine, guanine, and adenine has been investigated by using the ab initio Car−Parrinello molecular dynamicsmethod. It is demonstrated that all nucleic acid bases are highly flexible molecules and possess a nonplanareffective conformation of the pyrimidine ring despite the fact that the planar geometry corresponds to aminimum on the potential energy surface. The population of the planar geometry of the pyrimidine ring doesnot exceed 30%. Among the nonplanar conformations of the pyrimidine rings, the boat-like and half-chairconformations are the most populated.
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